Data from the Department for Education shows the equivalent of 0.3 per cent of pupils attending academies in 2009/10 – the latest available figures – were permanently barred from lessons compared with a national average of just 0.07 per cent.

A further 14.7 per cent of pupils were suspended – three times the total nationally.

Persistent bad behaviour was named as the main reason for permanent and temporary exclusions, followed by physical assaults on teachers and fellow pupils.

Officials insist that many of the schools covered by the research are disproportionately situated in deprived postcodes with large numbers of problem pupils – skewing the figures.

But further research from the DfE – comparing sponsored academies with other schools “in similar circumstances” – shows academies are still more likely to exclude difficult children.

Academies are independent state schools given complete freedom from local authorities to control their own admissions and exclusions, as well as staff pay, the shape of the academic year and length of the school day. Most of the first wave opened under Labour were existing schools converted into academies under the leadership of a third party sponsor.

The Coalition is now significantly expanding the number of schools given academy status in a move it claims will put greater power in the hands of teachers and blunt the influence of town hall bureaucrats.

But critics seized on the latest figures, claiming academies were employing their independence to expel the worst pupils.

The Anti-Academies Alliance, which campaigns against the schools, seized said that “by overt and covert means the school population is massaged to remove those pupils who are considered less likely to do well in GCSEs and thus affect the academy’s ratings”.

According to figures, the equivalent of 4.5 per cent of pupils were suspended every day from state schools in 2009/10. But this increased to 14.7 per cent among academies.

Academies also expelled the equivalent of 0.3 per cent of pupils during the academic year – compared with 0.07 per cent nationally.

In a separate disclosure, the DfE compared 103 academies with the same number of local council-run schools containing pupils from the same social backgrounds.

It found that these academies had a permanent exclusion rate of 0.32 per cent compared with 0.25 per cent for other schools. Academies were also less likely to go through an entire year without expelling a single pupil.

A DfE spokesman said: “Academies replacing previously underperforming schools have a very similar exclusion rate as other schools in similar circumstances, but we expect there to be a decrease in exclusions once the academy is properly established and the school begins to improve.”